AMBER Archive (2008)

Subject: Re: AMBER: Imaging before HBond analysis?

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Fri Apr 11 2008 - 17:52:04 CDT

> If I can ask a semi-related question: when using the 'radial' command in
> ptraj, a 3rd column of data is produced. Is this 3rd column the number of
> neighbours (the occupancy) as determined by the standard equation:
>
> n(r) = 4*Pi*rho*int[g(x)*x^2*dx]
>
> where the integral is from 0 to r, rho is density, and g(x) is the radial
> distribution function? Please excuse the pseudo-matlab/latex equation! :-)

I believe this is what I was calculating in the third column; easiest way
to check is to look at the code in transformRadial in actions.c which I
think is doing what is expected (at least with the standard RDF).

- tec3
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